Two of the biggest factors in stock price are how much of your stock is owned and how much stock you own (buying your own stock obviously contributes to both of these, resulting in a very large increase in stock price). It's likely computers are simply buying stock earlier than you, raising their stock value in the process. Upgrading your colony is the other factor that will provide you with a large increase, although a $45k price sounds about right for a level 5 HQ.

It would be much easier for us to give situation specific explanation and/or advice if you provide some screenshots or preferably the replay. Replay files are located in Documents\My Games\Offworld.